ismapper
Tags: insertion sequence transposase mobile-genetic-elements sample-scope
Identify transposase insertion sites in bacterial genomes.
This subworkflow maps insertion sequence (IS) positions in bacterial genomes using ISMapper. The tool identifies transposase insertion sites from short read sequence data by mapping reads to reference sequences and detecting insertion sites with high precision.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads (not supported by ISMapper) |
lr | Long reads (not supported by ISMapper) |
reference: Path
insertions: Path
| Name | Type | Description |
|---|---|---|
reference | Path | Reference genome in FASTA format for mapping |
insertions | Path | Insertion sequence reference file containing IS elements to map |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
supplemental | Directory containing the final tables of insertion sites and visual summaries |
run_outputs
No run-scope outputs.
Module Composition
This subworkflow calls the following modules:
- ismapper - Identify insertion sites and orientation of mobile genetic elements.
Used By
This subworkflow is used by the following workflows:
- ismapper - Identify insertion sequence positions in bacterial genomes.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
ISMapper
Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16, 667 (2015)